Dear Support,
We are finding that after we register our subjects' aCBF maps (produced by MRICloud software in native space) to the MNI brain, that the values are in some cases becoming negative. We started by l/r reversing our native M0 and aCBF maps for each subject (both generated by MRI Cloud), registered our aCBF maps to the MNI 2 mm brain with asl_reg using skull-stripped T1s for each subject that had been reoriented and registered to the MNI brain (12 dof with FLIRT), and then visually QC’d the registrations afterwards. We then extracted the values from the peak voxels in various ROIs, and found that many took on negative values (across several ROIs for most of our 38 longitudinal subjects: 33 at baseline and 31 at follow up). The MRI cloud generated aCBF maps in native space do not exhibit this behavior and have no negative values. Do you have any idea why we may be getting these negative values when we register the aCBF maps with asl_reg?
I will paste the command below for reference:
asl_reg -i PREV${i}_S${s}_ASL_real_aCBF_native_rpi.nii.gz --sbet PREV${i}_S${s}_T1_FS_RPI_MNI_brain.nii.gz -s PREV${i}_S${s}_T1_RPI_MNI_head.nii.gz -o asl_reg_aCBF-native_to_MNI
I read previously that using the perfusion image as the basis for registration was recommended, but did also test using flirt to 1) reg the M0 to the native T1 (6 dof), 2) reg the native T1 to MNI (12 dof), and then applied these transformations to the aCBF map, and found better registration results when using asl_reg.
If there is any other info I can provide that would be helpful, please let me know.
Thank you so much for your help!
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